PhredNtHash class #108
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PhredNtHash class #108
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parham-k
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Aug 3, 2023
| * @param seq_len Length of `seq`. | ||
| * @param hash_num Number of hashes to compute. | ||
| * @param k Length of k-mer. | ||
| * @param phred_min Minimum Phred score for a base to be included in the hash. |
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I think the explanation for phred_min needs clarification. I thought that if the Phred score for a base is less than this threshold, the k-mer will be ignored, not that specific base (unlike spaced seeds where bases are ignored).
| /** | ||
| * NtHash with Phred score filtering. | ||
| */ | ||
| class PhredNtHash : private NtHash |
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An alternative would be to use : public NtHash and hide unused methods with using, e.g.
private:
using NtHash::peek;
This way, there'll be no need to reimplement NtHash's public methods like get_pos etc.
Source: https://www.learncpp.com/cpp-tutorial/hiding-inherited-functionality/
| uint64_t get_reverse_hash() const { return NtHash::get_reverse_hash(); } | ||
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| private: | ||
| const char* qual_seq; |
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Let's prefer to use a shared_ptr or an std::string_view for qual_seq here.
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Added a new PhredNtHash that skip k-mers with any base with a lower quality than a user-specified Phred quality score.
Once the code change is approved, I will generate the docs, wrappers and python tests.